Exercises: LUMI Software Stacks¶

See the instructions to set up for the exercises.

Information in the LUMI Software Library¶

Search for information for the package GROMACS and quickly read through the page

Click to see the solution.

Link to the GROMACS documentation

It is an example of a package for which we have both user-level and some technical information. The page will first show some license information, then the actual user information which in this case also contains a link to training materials used by a course at CSC.

Newer versions of GROMACS for CPU are only compiled with the GNU compilers. Though it may be worthwhile to investigate if the Cray or AMD compilers offer better performance, it is outside the scope of what the main LUMI User Support Team can do given its small size and the amount of domain expertise needed to select a set of relevant benchmarks for GROMACS.

Using modules in the LUMI software stack¶

Search for the bzip2 tool (and not just the bunzip2 command as we also need the bzip2 command) and make sure that you can use software compiled with the Cray compilers in the LUMI stacks in the same session.
Click to see the solution.
```
module spider bzip2
```
shows that there are versions of bzip2 for several of the cpe* toolchains and in several versions of the LUMI software stack.

Of course we prefer to use a recent software stack, the 23.12 or 24.03 (and preferably the 24.03 as that is the best supported on at this time, early December 2024). Since we want to use other software compiled with the Cray compilers also, we really want a cpeCray version to avoid conflicts between different toolchains. So the module we want to load is bzip2/1.0.8-cpeCray-24.03.

To figure out how to load it, use
```
module spider bzip2/1.0.8-cpeCray-24.03
```
and see that (as expected from the name) we need to load LUMI/24.03 and can then use it in any of the partitions.

Installing software with EasyBuild¶

These exercises are based on material from the EasyBuild tutorials (and we have a special version for LUMI also).

Note: If you want to be able to uninstall all software installed through the exercises easily, we suggest you make a separate EasyBuild installation for the course, e.g., in /scratch/project_465001102/$USER/eb-course if you make the exercises during the course:

Start from a clean login shell with only the standard modules loaded.
Set EBU_USER_PREFIX:
```
export EBU_USER_PREFIX=/scratch/project_465001102/$USER/eb-course
```
You'll need to do that in every shell session where you want to install or use that software.
From now on you can again safely load the necessary LUMI and partition modules for the exercise.
At the end, when you don't need the software installation anymore, you can simply remove the directory that you just created.
```
rm -rf /scratch/project_465001102/$USER/eb-course
```

Installing a simple program without dependencies with EasyBuild¶

The LUMI Software Library contains the package eb-tutorial. Install the version of the package for the cpeCray toolchain in the 24.03 version of the software stack.

Click to see the solution.

We can check the eb-tutorial page in the LUMI Software Library if we want to see more information about the package.

You'll notice that there are versions of the EasyConfigs for cpeGNU, cpeCray and cpeAOCC. As we want to install software with the cpeCray toolchain for LUMI/24.03, we'll need the cpeCray-24.03 version which is the EasyConfig eb-tutorial-1.0.1-cpeCray-24.03.eb.
Obviously we need to load the LUMI/24.03 module. If we would like to install software for the CPU compute nodes, you need to also load partition/C. To be able to use EasyBuild, we also need the EasyBuild-user module.
```
module load LUMI/24.03 partition/C
module load EasyBuild-user
```
Now all we need to do is run the eb command from EasyBuild to install the software.

Let's however take the slow approach and first check if what dependencies the package needs:
```
eb eb-tutorial-1.0.1-cpeCray-24.03.eb -D
```
We can do this from any directory as the EasyConfig file is already in the LUMI Software Library and will be located automatically by EasyBuild. You'll see that all dependencies are already on the system so we can proceed with the installation:
```
eb eb-tutorial-1.0.1-cpeCray-24.03.eb 
```
After this you should have a module eb-tutorial/1.0.1-cpeCray-24.03 but it may not show up yet due to the caching of Lmod. Try
```
module av eb-tutorial/1.0.1-cpeCray-24.03
```
```
Now that we have the module, we can check what it actually does:
```
module help eb-tutorial/1.0.1-cpeCray-24.03
```
and we see that it provides the eb-tutorial command.
So let's now try to run this command:
```
module load eb-tutorial/1.0.1-cpeCray-24.03
eb-tutorial
```
Note that if you now want to install one of the other versions of this module, EasyBuild will complain that some modules are loaded that it doesn't like to see, including the eb-tutorial module and the cpeCray modules so it is better to unload those first:
```
module unload cpeCray eb-tutorial
```

Installing an EasyConfig given to you by LUMI User Support¶

Sometimes we have no solution ready in the LUMI Software Library, but we prepare one or more custom EasyBuild recipes for you. Let's mimic this case. In practice we would likely send those as attachments to a mail from the ticketing system and you would be asked to put them in a separate directory (basically since putting them at the top of your home directory would in some cases let EasyBuild search your whole home directory for dependencies which would be a very slow process).

You've been given two EasyConfig files to install a tool called py-eb-tutorial which is in fact a Python package that uses the eb-tutorial package installed in the previous exercise. These EasyConfig files are in the EasyBuild subdirectory of the exercises for this course. In the first exercise you are asked to install the version of py-eb-tutorial for the cpeCray/24.03 toolchain.

Click to see the solution.

Go to the EasyBuild subdirectory of the exercises and check that it indeed contains the py-eb-tutorial-1.0.0-cpeCray-24.03-cray-python-3.11.7.eb and py-eb-tutorial-1.0.0-cpeGNU-24.03-cray-python-3.11.7.eb files. It is the first one that we need for this exercise.

You can see that we have used a very long name as we are also using a version suffix to make clear which version of Python we'll be using.
Let's first check for the dependencies (out of curiosity):
```
eb py-eb-tutorial-1.0.0-cpeCray-24.03-cray-python-3.11.7.eb -D
```
and you'll see that all dependencies are found (at least if you made the previous exercise successfully). You may find it strange that it shows no Python module but that is because we are using the cray-python module which is not installed through EasyBuild and only known to EasyBuild as an external module.

And now we can install the package:

eb py-eb-tutorial-1.0.0-cpeCray-24.03-cray-python-3.11.7.eb

To use the package all we need to do is to load the module and to run the command that it defines:
```
module load py-eb-tutorial/1.0.0-cpeCray-24.03-cray-python-3.11.7
py-eb-tutorial
```
with the same remark as in the previous exercise if Lmod fails to find the module.

You may want to do this step in a separate terminal session set up the same way, or you will get an error message in the next exercise with EasyBuild complaining that there are some modules loaded that should not be loaded.

Installing software with uninstalled dependencies¶

Now you're asked to also install the version of py-eb-tutorial for the cpeGNU toolchain in LUMI/24.03 (and the solution given below assumes you haven'ty accidentally installed the wrong EasyBuild recipe in one of the previous two exercises).

Click to see the solution.

We again work in the same environment as in the previous two exercises. Nothing has changed here. Hence if not done yet we need
```
module load LUMI/24.03 partition/C
module load EasyBuild-user
```
Now go to the EasyBuild subdirectory of the exercises (if not there yet from the previous exercise) and check what the py-eb-tutorial-1.0.0-cpeGNU-24.03-cray-python-3.11.7.eb needs:
```
eb py-eb-tutorial-1.0.0-cpeGNU-24.03-cray-python-3.11.7.eb -D
```
We'll now see that there are two missing modules. Not only is the py-eb-tutorial/1.0.0-cpeGNU-24.03-cray-python-3.11.7 that we try to install missing, but also the eb-tutorial/1.0.1-cpeGNU-24.03. EasyBuild does however manage to find a recipe from which this module can be built in the pre-installed build recipes.
We can install both packages separately, but it is perfectly possible to install both packages in a single eb command by using the -r option to tell EasyBuild to also install all dependencies.
```
eb py-eb-tutorial-1.0.0-cpeGNU-24.03-cray-python-3.11.7.eb -r
```
At the end you'll now notice (with module avail) that both the module eb-tutorial/1.0.1-cpeGNU-24.03 and py-eb-tutorial/1.0.0-cpeGNU-24.03-cray-python-3.11.7 are now present.

To run you can use
```
module load py-eb-tutorial/1.0.0-cpeGNU-24.03-cray-python-3.11.7
py-eb-tutorial
```